Mitochondrial genome and transcription of Shiraia-like species reveal evolutionary aspects in protein-coding genes

<i>Shiraia</i>-related species are well-known bambusicolous fungi in <i>Dothideomycetes</i> class, with high value in traditional medicine for producing hypocrellin, as an anticipated photosensitiser. The complete mitogenomes of hypocrellin-producing <i>Pseudoshiraiaconidialis</i> strains were analysed in the present study, with functional gene variations through comparative genomics and transcriptomics. Five strains (ZZZ816, CNUCC1353PR, JAP103846, CNUCC C72, CNUCC C151) were sequenced, which indicated similar genome characteristics. Two of them possess an extra <i>atp6</i> gene, and the associated variable fragment "<i>HSP1-HSP2-atp6_2</i>" correlates closely with hypocrellin production capacity. Therefore, these five strains were divided into three groups: ZZZ816 and CNUCC1353PR possessing high production efficiency, CNUCC C72 and JAP103846 with low yield and CNUCC C151 as a transition type. The gene expression changes were screened under various conditions. ZZZ816-related species showed significant changes in mitochondrial genes, especially <i>HSP1</i>, <i>HSP2</i> and <i>atp6_2</i>, linked closely to hypocrellin synthesis and stress response; <i>rps3</i> expression also consistently correlated with hypocrellin production. JAP103846 group showed a stable expression pattern divergently, except for <i>rps3</i> suppression by blue light. These findings would provide new insights into secondary metabolite regulation and ROS resistance. Above all, this study conducted the comprehensive analysis of <i>Shiraia</i>-like fungi mitogenomes and functional gene expression, which can update the understanding of fungal evolution and potential for improved hypocrellin production.